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- PDB-7bgn: Crystal structure of MtHISN2-AMP complex, a bifunctional enzyme f... -

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データを開く


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読み込み中...

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基本情報

登録情報
データベース: PDB / ID: 7bgn
タイトルCrystal structure of MtHISN2-AMP complex, a bifunctional enzyme from the histidine biosynthetic pathway
要素Phosphoribosyl-AMP cyclohydrolase
キーワードHYDROLASE / Histidine / Pyrophosphohydrolase / Cyclohydrolase / Bifunctional / PRA-CH / PRA-PH / AMP
機能・相同性
機能・相同性情報


phosphoribosyl-AMP cyclohydrolase activity / phosphoribosyl-ATP diphosphatase activity / L-histidine biosynthetic process / ATP binding / metal ion binding
類似検索 - 分子機能
Phosphoribosyl-AMP cyclohydrolase domain / Phosphoribosyl-AMP cyclohydrolase domain superfamily / Phosphoribosyl-AMP cyclohydrolase / Phosphoribosyl-ATP pyrophosphohydrolase / Phosphoribosyl-ATP pyrophosphohydrolase-like / Phosphoribosyl-ATP pyrophosphohydrolase
類似検索 - ドメイン・相同性
ADENOSINE MONOPHOSPHATE / Histidine biosynthesis hisIE protein
類似検索 - 構成要素
生物種Medicago truncatula (タルウマゴヤシ)
手法X線回折 / シンクロトロン / 単波長異常分散 / 解像度: 2.7 Å
データ登録者Witek, W. / Ruszkowski, M.
資金援助 ポーランド, 1件
組織認可番号国
Polish National Science CentreSONATA 2018/31/D/NZ1/03630 ポーランド
引用ジャーナル: Sci Rep / 年: 2021
タイトル: Structural and mechanistic insights into the bifunctional HISN2 enzyme catalyzing the second and third steps of histidine biosynthesis in plants.
著者: Witek, W. / Sliwiak, J. / Ruszkowski, M.
履歴
登録2021年1月8日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02021年5月19日Provider: repository / タイプ: Initial release
改定 1.12024年5月15日Group: Data collection / Database references / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

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集合体

登録構造単位
A: Phosphoribosyl-AMP cyclohydrolase
B: Phosphoribosyl-AMP cyclohydrolase
C: Phosphoribosyl-AMP cyclohydrolase
D: Phosphoribosyl-AMP cyclohydrolase
E: Phosphoribosyl-AMP cyclohydrolase
F: Phosphoribosyl-AMP cyclohydrolase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)165,35838
ポリマ－160,1526
非ポリマー5,20532
水1,11762
1
A: Phosphoribosyl-AMP cyclohydrolase
B: Phosphoribosyl-AMP cyclohydrolase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)54,84312
ポリマ－53,3842
非ポリマー1,45810
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area10180 Å2
ΔGint-293 kcal/mol
Surface area17580 Å2
手法PISA
2
C: Phosphoribosyl-AMP cyclohydrolase
D: Phosphoribosyl-AMP cyclohydrolase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)55,25813
ポリマ－53,3842
非ポリマー1,87311
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area10780 Å2
ΔGint-285 kcal/mol
Surface area17400 Å2
手法PISA
3
E: Phosphoribosyl-AMP cyclohydrolase
F: Phosphoribosyl-AMP cyclohydrolase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)55,25813
ポリマ－53,3842
非ポリマー1,87311
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area10850 Å2
ΔGint-297 kcal/mol
Surface area17620 Å2
手法PISA
単位格子
Length a, b, c (Å)200.892, 67.970, 134.237
Angle α, β, γ (deg.)90.000, 128.927, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID
11
21
31
41
51
61

NCSドメイン領域:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAASPASP(chain 'A' and (resid 48 through 156 or resid 166...AA48 - 1563 - 111
12ASNASNVALVAL(chain 'A' and (resid 48 through 156 or resid 166...AA166 - 187121 - 142
13SERSERPHEPHE(chain 'A' and (resid 48 through 156 or resid 166...AA195 - 264150 - 219
14HOHHOHHOHHOH(chain 'A' and (resid 48 through 156 or resid 166...AMA401
25ALAALAASPASP(chain 'B' and (resid 48 through 156 or resid 166...BB48 - 1563 - 111
26ASNASNVALVAL(chain 'B' and (resid 48 through 156 or resid 166...BB166 - 187121 - 142
27SERSERPHEPHE(chain 'B' and (resid 48 through 156 or resid 166...BB195 - 264150 - 219
28HOHHOHHOHHOH(chain 'B' and (resid 48 through 156 or resid 166...BNA401
39ALAALAASPASP(chain 'C' and (resid 48 through 156 or resid 166 through 264 or resid 301 through 401))CC48 - 1563 - 111
310ASNASNVALVAL(chain 'C' and (resid 48 through 156 or resid 166 through 264 or resid 301 through 401))CC166 - 187121 - 142
311SERSERPHEPHE(chain 'C' and (resid 48 through 156 or resid 166 through 264 or resid 301 through 401))CC195 - 264150 - 219
312HOHHOHHOHHOH(chain 'C' and (resid 48 through 156 or resid 166 through 264 or resid 301 through 401))COA401
413ALAALAASPASP(chain 'D' and (resid 48 through 156 or resid 166 through 264 or resid 301 through 401))DD48 - 1563 - 111
414ASNASNVALVAL(chain 'D' and (resid 48 through 156 or resid 166 through 264 or resid 301 through 401))DD166 - 187121 - 142
415SERSERPHEPHE(chain 'D' and (resid 48 through 156 or resid 166 through 264 or resid 301 through 401))DD195 - 264150 - 219
416HOHHOHHOHHOH(chain 'D' and (resid 48 through 156 or resid 166 through 264 or resid 301 through 401))DPA401
517ALAALAASPASP(chain 'E' and (resid 48 through 264 or resid 301 through 401))EE48 - 1563 - 111
518ASNASNVALVAL(chain 'E' and (resid 48 through 264 or resid 301 through 401))EE166 - 187121 - 142
519SERSERPHEPHE(chain 'E' and (resid 48 through 264 or resid 301 through 401))EE195 - 264150 - 219
520HOHHOHHOHHOH(chain 'E' and (resid 48 through 264 or resid 301 through 401))EQA401
621ALAALAASPASP(chain 'F' and (resid 48 through 156 or resid 166...FF48 - 1563 - 111
622ASNASNVALVAL(chain 'F' and (resid 48 through 156 or resid 166...FF166 - 187121 - 142
623SERSERPHEPHE(chain 'F' and (resid 48 through 156 or resid 166...FF195 - 264150 - 219
624HOHHOHHOHHOH(chain 'F' and (resid 48 through 156 or resid 166...FRA401

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要素

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タンパク質 , 1種, 6分子 ABCDEF

#1: タンパク質
Phosphoribosyl-AMP cyclohydrolase


分子量: 26692.064 Da / 分子数: 6 / 由来タイプ: 組換発現 / 詳細: Without a signal peptide (residues 1-47)
由来: (組換発現) Medicago truncatula (タルウマゴヤシ)
遺伝子: 25498966, MTR_7g084480, MtrunA17_Chr7g0252441 / プラスミド: pMCSG68
発現宿主: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (大腸菌)
参照: UniProt: A0A072U2X9, phosphoribosyl-AMP cyclohydrolase, phosphoribosyl-ATP diphosphatase

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非ポリマー , 5種, 94分子

#2: 化合物
ChemComp-ZN / ZINC ION


分子量: 65.409 Da / 分子数: 18 / 由来タイプ: 合成 / 式: Zn
#3: 化合物
ChemComp-AMP / ADENOSINE MONOPHOSPHATE


分子量: 347.221 Da / 分子数: 11 / 由来タイプ: 合成 / 式: C10H14N5O7P / タイプ: SUBJECT OF INVESTIGATION / コメント: AMP*YM
#4: 化合物 ChemComp-MG / MAGNESIUM ION


分子量: 24.305 Da / 分子数: 1 / 由来タイプ: 合成 / 式: Mg
#5: 化合物 ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


分子量: 92.094 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C3H8O3
#6: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 62 / 由来タイプ: 天然 / 式: H2O

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詳細

研究の焦点であるリガンドがあるかY

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実験情報

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実験

実験手法: X線回折 / 使用した結晶の数: 1

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試料調製

結晶マシュー密度: 2.23 Å3/Da / 溶媒含有率: 44.74 %
結晶化温度: 291 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 7.5
詳細: 0.2 M potassium iodide, 20% Polyethylene glycol 3350, 10 mM MgCl2, 0.1 mM ZnCl2, and 20 mM AMP (added in 100 mM Hepes pH 7.5), 7.5% glycerol

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データ収集

回折平均測定温度: 100 K / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: APS / ビームライン: 22-ID / 波長: 1 Å
検出器タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2018年12月13日
放射モノクロメーター: Si(111) / プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 1 Å / 相対比: 1
反射解像度: 2.7→48.45 Å / Num. obs: 33411 / % possible obs: 94.1 % / 冗長度: 3.9 % / Biso Wilson estimate: 57.24 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.091 / Net I/σ(I): 11.1
反射 シェル

Diffraction-ID: 1

解像度 (Å)冗長度 (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2% possible all
7.83-48.453.50.0328.758480.99999.2
2.7-2.854.10.73267250.67555.8

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解析

ソフトウェア
名称バージョン分類
PHENIX1.17.1_3660精密化
XDSデータ削減
Cootモデル構築
PHENIXAutobuildモデル構築
AutoSol位相決定
精密化構造決定の手法: 単波長異常分散 / 解像度: 2.7→39.07 Å / SU ML: 0.3726 / 交差検証法: FREE R-VALUE / 位相誤差: 28.2922
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2458 1010 3.02 %
Rwork0.1813 32395 -
obs0.1832 33405 81.99 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
原子変位パラメータBiso mean: 61.85 Å2
精密化ステップサイクル: LAST / 解像度: 2.7→39.07 Å
タンパク質核酸リガンド溶媒全体
原子数9658 0 284 62 10004
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.005910073
X-RAY DIFFRACTIONf_angle_d0.770913663
X-RAY DIFFRACTIONf_chiral_restr0.04881612
X-RAY DIFFRACTIONf_plane_restr0.00451699
X-RAY DIFFRACTIONf_dihedral_angle_d17.70353814
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.80.3826190.3395713X-RAY DIFFRACTION12.69
2.8-2.980.37921170.29313591X-RAY DIFFRACTION64.43
2.98-3.210.35351710.26175437X-RAY DIFFRACTION96.81
3.21-3.530.27161740.20675619X-RAY DIFFRACTION99.9
3.53-4.040.23281710.17555622X-RAY DIFFRACTION99.81
4.04-5.090.21091780.13715644X-RAY DIFFRACTION99.81
5.09-39.070.20731800.16515769X-RAY DIFFRACTION99.43
精密化 TLS

手法: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.84116491084-1.52127339173-0.2180687856023.250598853630.4586650678575.12065210944-0.065911193251.50634433332-0.573533815261-0.7364703964390.259379144917-0.935285198211-0.01244096419780.822403310449-0.1339610699920.539070170116-0.09274707353330.2012980782690.820901783854-0.2175124922050.687051164285-13.233185324532.49803813762.75777773164
28.439296185091.536221799950.6112147650034.398997714451.998619676047.69636095539-0.57708978890.690243556461-0.484269176945-0.4099749883410.531144813554-0.750045406682-0.05773421368630.954698399291-0.003622409730230.3925981913740.005297424996190.09100208161620.467339345535-0.02611035662470.632685021795-12.325068086534.07966103918.61125084723
37.699298623113.384576113660.5806852757262.15942978634-0.9702864780972.627130385350.0380993352124-0.2395459431740.714499089329-0.334872706310.06311733194350.0347871359235-0.3276836388430.163602902275-0.04583420774120.576039498867-0.06491850838030.1421632006630.357049338273-0.03066291771570.53349630274-23.08405151246.625297743616.1287475622
47.96122324928-0.182860817642-4.578604993186.960925724090.4621881171087.207323655130.152457318627-0.366395697531.424437356440.715540640592-0.21547753423-0.20026220773-1.06924202744-0.1257300664770.01056982591180.4769563996160.0750892025732-0.1137637357920.301973226172-0.09151993603150.527811484055-37.939315749642.893899819730.8271327094
54.88908432008-1.076125236651.141826465223.286200796381.079126369222.440701690770.0218912349626-0.375242212715-0.1963026861990.288341074908-0.2038161537810.1287703290750.191766170584-0.1557538106180.1817539102050.408682006634-0.0103089656920.06200279735580.2259558447330.06283691616580.321293161577-41.291459905828.347860319426.7510799562
63.224753176720.8508465318830.394365066324.5447597466-2.264509943843.43275450207-0.3356370226931.10212103020.40767104008-0.5494594571850.255064048954-0.0528396536747-0.4751606572320.3530830024530.125546417670.589032993835-0.128612911594-0.03591217835640.6063610928970.1006101473840.341790496654-28.659981344946.6556152488-0.0270039097896
76.61428647584-0.431921391485-0.528214461714.581090020331.083681937447.86581307720.5382062124860.425792090865-0.211941471555-0.6079219074420.350823316005-0.5801582771730.9276225831270.371692332103-0.8276496294040.640734075694-0.06983172871030.06204915211480.550624372513-0.215688297080.485387066566-27.040647635926.37514187970.850417530293
87.900581002030.888844919936-1.474709805042.023679651170.2521548743428.161267229310.1481848171870.658080037126-1.00659914025-0.5682086842960.31095164037-0.2432357533071.063962380780.173120657711-0.3657956611560.520282364031-0.00120626848835-0.006343408064640.272159023896-0.05714498711450.492858956075-37.081826520414.347980375315.4623213201
93.945320463710.3760419243540.9958004535495.386611089550.5846367373193.784408162070.106446847094-0.310694787145-0.4071808039840.4126173828790.09023821167990.01815643934320.39402105261-0.192145237525-0.1906550456510.2366510151980.02981313121460.03447024244370.2191082141980.05540864699160.284561980992-39.655017171824.829617780526.0954030939
103.48697685167-0.344360094072-0.5020491645670.7320314871321.385332352646.48491631205-0.0786697435628-0.439875487794-0.274567555610.2394349671640.0975115076040.1554487890460.0489538526168-0.643063784935-0.0169999906940.530291399911-0.01939798549290.01470438575040.3727954452260.1864289319550.578417437016-31.95191933750.82274860739543.1490328888
113.229281279041.722416737231.042409707621.021694675631.305319581214.89573015134-0.03325487436870.04312702770110.0586291769663-0.04678308860980.07506473788840.05117532109610.0828535086594-0.05787539735380.02566432101440.3638591628770.07264031956680.03062262492630.2431895213190.06967267552790.510751790867-25.85770687243.0324401166438.9528441748
120.187792806409-0.475018059951-0.3945653941042.472457215463.947638549847.38312441669-0.1791731630530.3394367571631.02554407317-0.5931697121560.0749661281537-0.441822964164-0.9868234646350.2969091466810.0906773904550.78059931385-0.0551934107764-0.07729964322590.4659387305450.2546050621720.686780206391-16.388780942816.016924897233.3611398828
132.7038109529-1.00005070319-0.4261778224186.41958974875-0.5937250272325.52442825629-0.04583356074950.521502802070.236136893331-0.7633311308010.153287850253-0.719171326884-0.1642900232720.592173578263-0.06488001729930.373381658968-0.2221759901060.03924055593150.486485075773-0.03965064881850.541977407587-0.527530289228-0.33635916556718.3284616601
140.672596977888-1.02475641809-0.244145815834.05290967468-2.80479011824.17269432554-0.170586711618-0.0388968198180.518805293774-0.0921169009611-0.0531365833125-0.455820605071-0.483874171710.5217784996290.3093800043620.453837894527-0.1539838749880.01639270313110.495707421638-0.07837997689750.497987780572-0.669349866547-2.6395281489523.1689168961
158.583216642921.17778481833-5.15321094272.948660583043.594482251529.65503239971-0.305364977130.5680375563170.134767480108-0.2531969226760.1210244559690.695847349323-0.201597792887-0.3862531952050.158110942790.305252876216-0.0202886678321-0.1073321913550.322898688320.06750232483110.429037513511-17.3778042088-7.0967251523523.5883501248
168.74975670911-1.9002596171.743416148765.043814715082.333627059826.83122158373-0.7237344191660.3510121758031.450589894480.9957395152980.359513022605-0.447765410577-1.418804634030.507820020460.2556058330140.786869562433-0.0654090562899-0.1675076715780.5061188614530.1791660921840.79903056828-20.891643824324.574840136446.3901252408
173.19563145304-2.60581329478-3.10479646372.498995038312.211163662439.172819177-0.0992410436283-0.702135701860.4939611714630.05477184909450.354254390524-0.619606488024-0.6396443398060.335533847274-0.063154531440.4740695785330.00285200637746-0.07359350144880.371730325584-0.0001571171031260.485334266027-14.392994558312.296774229946.2397452369
186.30757285283-2.47858705151.864372962245.492612348981.638118806955.06677278356-0.103062461185-0.3948658573430.1891332100380.7485325414350.3099921785840.144295283576-0.224113897784-1.13851081874-0.3039754802870.7903376399670.0841490896683-0.1803809789210.4720220503720.1257890417960.603152328933-13.326007507413.953271182855.1587518433
196.77584661855-0.7167053062781.142289065074.464240648231.010656526854.416468505770.1288732449240.1338052243940.154364788326-0.491741159192-0.0445746251072-0.469396483958-0.2882517241270.653980250897-0.04749503971070.436120835077-0.0816275905765-0.002354059177740.3268840750140.08024642954950.406752155017-11.984829042311.822473508444.4559886032
205.316040576870.483762191318-0.3358229573911.451152471782.493969519784.558980119990.29317918977-0.0853133043454-0.743085680061.782668742020.275984801351-0.3880967154740.3904596133770.581937292808-0.3430717429420.688328547370.08787514033840.07037681621670.4853105528370.1658653201340.68954525417-8.40540795351-0.39089290669151.6752379681
217.318548274062.11535302635-3.022027882941.64536920532-2.11857589585.69312607556-0.345211807339-0.762641210826-1.34643501842-0.193529037680.331556091606-0.399070752340.590961874398-0.445700432791-0.01631485975510.6143198381430.05116548163060.03406315717660.4544978733940.2412616308510.644781848684-19.4552104901-7.7173734257546.3874788425
229.595893769040.5430638071584.223278880944.35094254256-4.769878120567.67319404749-0.370415539972-1.26409541705-0.762007589124-0.02580906571520.8081726988390.3597108014250.385940568829-0.716348545622-0.4101861480470.4665863259790.03065640880250.04975275107590.3989475221180.09113195533870.615278998657-9.29933976367-14.922117789136.8677962825
232.77720194638-0.489472911117-2.518493829068.23175346232-1.715547213892.87365327808-0.474023359369-0.0895378088558-1.099826775-1.05638062022-0.221411710489-0.03153338992521.620812474890.524544949650.7478862953620.6196433506480.1522260391350.1184605429530.6675746393620.02885374044040.729565904084-4.25319407205-24.624806886330.3597677805
245.02614911944-0.9004007020741.328566250452.247158491440.2219476668254.82592369069-0.09415769559580.174705358945-0.810739385532-0.3979219709180.320987626494-0.2432722495850.3057401944680.0631865961864-0.245323290680.42434821893-0.1112242192020.01158979687580.319649679354-0.02263412806580.589213609821-6.26133319878-13.063698297718.5869883911
254.15204512932-2.64348785528-1.876490625779.662907691533.067925394213.90384662884-0.235466450922-0.342212965260.094487437494-0.3207399334440.24011887982-0.9922230884090.01665764929520.784140966462-0.02497768719440.344541717194-0.105651889453-0.04313485111770.482564865963-0.001753935953840.529490878187-0.403394136739-0.57272751734233.2268095442
262.86359606885-2.788725095180.4669728397647.645729775270.8067001843022.083244695520.2476876771660.673185627311-0.379903165058-0.225381634705-0.2967756165460.05004508508710.4139973626560.0480758327297-0.0006095117015010.384402697461-0.1531938311690.02975949200080.563870151851-0.2452623036340.47186589288929.7484515104-1.4122304931514.5831615024
274.22030781627-1.351589210424.285047284923.573195184220.3751168924375.523122233760.1675647469420.676733741043-0.71025504706-0.145327086381-0.4744617528971.031746476160.309643162421-0.3518283418480.2712277401710.332880792357-0.0876760478490.01809720978150.562503970391-0.1955902172510.51335745388424.05542667291.4478181931714.8921682891
284.63730012376-0.7901833021060.369852464265.744947223420.6992522318130.681048752124-0.106087711337-0.609143455039-0.3337181802350.437380865057-0.4745730707121.13162456957-0.0115788581375-0.4435316643650.5704719553940.402749871325-0.05351694164060.1805583860820.719152104807-0.1799503985490.68033150818716.146240390510.58045113432.9560745256
293.91517163958-0.337048282304-1.451328799682.98439818862-0.2424920347412.38032559369-0.0990542964404-0.492844318040.7196689487730.299433015545-0.1236709720230.431977492881-0.557468034916-0.3170428414470.1098965895240.4928959286470.1382977393990.02991185698470.510693619069-0.2006482085490.43020317386124.95085822632.890276416638.6386361535
300.9629754376461.78611502861-1.767903601999.018193475890.2488115698338.583870139480.248105610105-0.004751269912520.00639812614539-0.278531979427-0.5140849571180.320557723144-1.11988441682-0.1570615805790.3223537476860.3298897977210.0913890279391-0.2065061390070.510978510425-0.1048405837430.43252285477721.755330650323.650376932521.1039522822
316.421647997370.6063188691030.3001260101122.33407956059-0.6198734737493.03545309473-0.0155707483237-0.417111154584-1.049439185670.460120699574-0.1508521142550.2940183763840.480905088553-0.3531941224750.1362557579130.470800444311-0.0194500051840.1446869521990.396867421226-0.01013291479670.45545377955830.1172519304-3.3391484029635.9752643102
326.753859943480.2130274090451.875658719285.83429228121.356620646421.00202003004-0.009322198516420.7203428279110.510236944875-0.130042062474-0.331845100838-0.1038889691020.05463366538290.008749806357660.3280532197940.389837428061-0.07105396050310.1141297936480.5242678908950.03543619065330.33188961316239.96989055897.2933652174621.8067579956
332.922730078792.228543759110.6036485693335.37847387571-0.130311048746.83768451547-0.2632179490850.6120367152230.146637756376-0.923950798227-0.0933477132423-0.659647929623-0.5743410529120.5841766437740.4031720205440.4599216982330.04192633083490.003353398064620.4284085004180.07461500927420.47240638090441.900134871129.164271489120.0426236057
344.115072624240.285746907619-1.013201438235.14181761493-0.9113706698493.02930586716-0.006548104534850.3110920136720.4536327265840.0757372841634-0.2900444929570.410124156045-0.654735660968-0.4787936939370.2323146133660.3893491069790.0831959128612-0.07968637003120.404607393887-0.1784489233670.35495928646127.834903777831.641537063629.5082403345
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 48 through 93 )
2X-RAY DIFFRACTION2chain 'A' and (resid 94 through 137 )
3X-RAY DIFFRACTION3chain 'A' and (resid 138 through 171 )
4X-RAY DIFFRACTION4chain 'A' and (resid 172 through 203 )
5X-RAY DIFFRACTION5chain 'A' and (resid 204 through 264 )
6X-RAY DIFFRACTION6chain 'B' and (resid 47 through 137 )
7X-RAY DIFFRACTION7chain 'B' and (resid 138 through 171 )
8X-RAY DIFFRACTION8chain 'B' and (resid 172 through 203 )
9X-RAY DIFFRACTION9chain 'B' and (resid 204 through 264 )
10X-RAY DIFFRACTION10chain 'C' and (resid 47 through 124 )
11X-RAY DIFFRACTION11chain 'C' and (resid 125 through 147 )
12X-RAY DIFFRACTION12chain 'C' and (resid 148 through 171 )
13X-RAY DIFFRACTION13chain 'C' and (resid 172 through 227 )
14X-RAY DIFFRACTION14chain 'C' and (resid 228 through 248 )
15X-RAY DIFFRACTION15chain 'C' and (resid 249 through 264 )
16X-RAY DIFFRACTION16chain 'D' and (resid 47 through 62 )
17X-RAY DIFFRACTION17chain 'D' and (resid 63 through 93 )
18X-RAY DIFFRACTION18chain 'D' and (resid 94 through 108 )
19X-RAY DIFFRACTION19chain 'D' and (resid 109 through 137 )
20X-RAY DIFFRACTION20chain 'D' and (resid 138 through 147 )
21X-RAY DIFFRACTION21chain 'D' and (resid 148 through 171 )
22X-RAY DIFFRACTION22chain 'D' and (resid 172 through 186 )
23X-RAY DIFFRACTION23chain 'D' and (resid 187 through 203 )
24X-RAY DIFFRACTION24chain 'D' and (resid 204 through 248 )
25X-RAY DIFFRACTION25chain 'D' and (resid 249 through 264 )
26X-RAY DIFFRACTION26chain 'E' and (resid 47 through 93 )
27X-RAY DIFFRACTION27chain 'E' and (resid 94 through 137 )
28X-RAY DIFFRACTION28chain 'E' and (resid 138 through 186 )
29X-RAY DIFFRACTION29chain 'E' and (resid 187 through 248 )
30X-RAY DIFFRACTION30chain 'E' and (resid 249 through 264 )
31X-RAY DIFFRACTION31chain 'F' and (resid 47 through 137 )
32X-RAY DIFFRACTION32chain 'F' and (resid 138 through 171 )
33X-RAY DIFFRACTION33chain 'F' and (resid 172 through 203 )
34X-RAY DIFFRACTION34chain 'F' and (resid 204 through 264 )

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万見について

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お知らせ

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2022年2月9日: EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

  • EMDBのヘッダファイルのバージョン3が、公式のフォーマットとなりました。
  • これまでは公式だったバージョン1.9は、アーカイブから削除されます。

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

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2020年8月12日: 新型コロナ情報

新型コロナ情報

URL: https://pdbj.org/emnavi/covid19.php

新ページ: EM Navigatorに新型コロナウイルスの特設ページを開設しました。

関連情報:Covid-19情報 / 2020年3月5日: 新型コロナウイルスの構造データ

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2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

外部リンク:COVID-19特集ページ - PDBj / 今月の分子2020年2月：コロナウイルスプロテーアーゼ

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2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

  • EMDBエントリに付与されているアクセスコード(EMDB-ID)は4桁の数字(例、EMD-1234)でしたが、間もなく枯渇します。これまでの4桁のID番号は4桁のまま変更されませんが、4桁の数字を使い切った後に発行されるIDは5桁以上の数字(例、EMD-12345)になります。5桁のIDは2019年の春頃から発行される見通しです。
  • EM Navigator/万見では、接頭語「EMD-」は省略されています。

関連情報:Q: 「EMD」とは何ですか？ / 万見/EM NavigatorにおけるID/アクセスコードの表記

外部リンク:EMDB Accession Codes are Changing Soon! / PDBjへお問い合わせ

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2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

  • 新バージョンのPDBx/mmCIF辞書形式に基づくデータがリリースされました。
  • 今回の更新はバージョン番号が4から5になる大規模なもので、全エントリデータの書き換えが行われる「Remediation」というアップデートに該当します。
  • このバージョンアップで、電子顕微鏡の実験手法に関する多くの項目の書式が改定されました(例：em_softwareなど)。
  • EM NavigatorとYorodumiでも、この改定に基づいた表示内容になります。

外部リンク:wwPDB Remediation / OneDepデータ基準に準拠した、より強化された内容のモデル構造ファイルが、PDBアーカイブで公開されました。

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万見 (Yorodumi)

幾万の構造データを、幾万の視点から

  • 万見(Yorodumi)は、EMDB/PDB/SASBDBなどの構造データを閲覧するためのページです。
  • EM Navigatorの詳細ページの後継、Omokage検索のフロントエンドも兼ねています。

関連情報:EMDB / PDB / SASBDB / 3つのデータバンクの比較 / 万見検索 / 2016年8月31日: 新しいEM Navigatorと万見 / 万見文献 / Jmol/JSmol / 機能・相同性情報 / 新しいEM Navigatorと万見の変更点

他の情報も見る